US9732391B2 - Cichorium spp. male sterile mutants - Google Patents
Cichorium spp. male sterile mutants Download PDFInfo
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- US9732391B2 US9732391B2 US14/091,051 US201314091051A US9732391B2 US 9732391 B2 US9732391 B2 US 9732391B2 US 201314091051 A US201314091051 A US 201314091051A US 9732391 B2 US9732391 B2 US 9732391B2
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Images
Classifications
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- A—HUMAN NECESSITIES
- A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
- A01H—NEW PLANTS OR NON-TRANSGENIC PROCESSES FOR OBTAINING THEM; PLANT REPRODUCTION BY TISSUE CULTURE TECHNIQUES
- A01H5/00—Angiosperms, i.e. flowering plants, characterised by their plant parts; Angiosperms characterised otherwise than by their botanic taxonomy
- A01H5/02—Flowers
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
- C12Q1/6895—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for plants, fungi or algae
-
- A—HUMAN NECESSITIES
- A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
- A01H—NEW PLANTS OR NON-TRANSGENIC PROCESSES FOR OBTAINING THEM; PLANT REPRODUCTION BY TISSUE CULTURE TECHNIQUES
- A01H1/00—Processes for modifying genotypes ; Plants characterised by associated natural traits
- A01H1/04—Processes of selection involving genotypic or phenotypic markers; Methods of using phenotypic markers for selection
-
- A01H5/025—
-
- A—HUMAN NECESSITIES
- A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
- A01H—NEW PLANTS OR NON-TRANSGENIC PROCESSES FOR OBTAINING THEM; PLANT REPRODUCTION BY TISSUE CULTURE TECHNIQUES
- A01H6/00—Angiosperms, i.e. flowering plants, characterised by their botanic taxonomy
- A01H6/14—Asteraceae or Compositae, e.g. safflower, sunflower, artichoke or lettuce
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
- C12N15/09—Recombinant DNA-technology
- C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
- C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
- C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
- C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
- C12N15/8261—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield
- C12N15/8287—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for fertility modification, e.g. apomixis
- C12N15/8289—Male sterility
Definitions
- the present invention relates to Cichorium spp. nuclear recessive male sterile mutants of Cichorium intybus subsp. intybus var. foliosum (also known as leaf chicory), to newly identified polymorphic molecular markers tightly linked to the nuclear recessive gene that control the expression of the male sterile trait in leaf chicory, to methods for the selection of nuclear recessive male sterile mutants in leaf chicory, to methods for the production of inbred lines of leaf chicory showing male sterility (i.e. seed parent) and male fertility (i.e. pollen parent) of leaf chicory, including all cultivated types of Radicchio, and to F1 hybrids that are heterozygous at the locus for male sterility, being so characterized by male fertility.
- breeding programs avail themselves more and more frequently of molecular genetics techniques that allow the breeders to carry out a precise selection and/or production of plants expressing the desired characters (corresponding to specific genotypes that combine superior alleles for a number of genes), the techniques being particularly efficient when molecular markers linked to the loci of the genes of interest, said markers being polymorphic and allowing the tracking of the alleles and traits of interest.
- markers with co-dominant inheritance patterns are of particular interest in order to allow a correct selection of the specific alleles and genotypes desired.
- a tight linkage of the marker to the locus of interest will result in the co-segregation of a specific allele of the marker with a specific allele of the gene mapping in said locus, thus allowing a very refined tracking of the desired allele/s at that locus. It is therefore essential to identify reliable molecular markers for characters that may be desirable, in particular when the characters of interest are genetically recessive.
- F1 hybrids are populations of plants of high commercial interest manifesting extreme vigour, being highly heterozygous (for most of the genes or at least heterozygous for the genes of interest). More precisely, for F1 hybrid plants the term “heterosis” is used, where this term officially indicates in genetics the greater vigour in terms of size, growth rate, resistance to biotic and abiotic stresses, and fertility and productivity of hybrids compared to their parental plants, usually stemmed from controlled crosses between highly inbred lines, which are homozygous for different alleles at each locus being considered. Consequently, heterosis is always associated with increased heterozygosity. These plants are known to produce an F2 progeny (and F3, F4, etc in the following generations) of much lower quality with respect to the F1 generation because of genetic segregation and recombination mechanisms.
- the loss of the traits of commercial interest in the generations after F1 is due to the high number of genes of interest for which the F1 plant is heterozygous and to the genetic recombination by means of independent assortment thereof, assortment that will randomly spread the alleles of the genes of interest thus providing F1+n (n ⁇ 1) genotypes that are not anymore carrying the desired genotype (and the resulting vigorous phenotype) of F1 in all the loci of interest.
- the seed producer parental line (also called “seed parent”) is preferably male sterile thus avoiding completely the occurrence of self-pollination and presence in the F1 generation of inbred progeny seeds in disadvantage to the production of F1 hybrids.
- seed parent also called “seed parent”
- the seed producer parental line is normally made male sterile by physical removal of the anthers from the flowers before pollen dispersal.
- male sterility genes i.e. genes responsible for the fertility of the male part of the flower that, upon mutation, can provide a male sterile plant would be preferable.
- cytoplasmic male sterility Two kinds of male sterility can be observed in plants: nuclear and cytoplasmic male sterility.
- the former type of genetic male sterility is based solely on recessive mutations that affect different functions in nuclear genes (ms indicates the recessive allele causing male sterility whereas Ms indicates the wild type dominant allele rendering the plant male fertile), while cytoplasmic male sterility (CMS) is maternally inherited and mainly due to mutations in the expression of mitochondrial genes that are inherited only maternally by the egg cell cytoplasm.
- CMS cytoplasmic male sterility
- Rf nuclear-encoded fertility restorer
- outcrossing is promoted by a floral morpho-phenology (i.e., proterandry, having the anthers mature before the pistils) unfavourable to selfing in the absence of pollen donors and by a favourable competition of allo-pollen grains and tubes (i.e., pollen genetically diverse from that produced by the seed parents, usually called auto-pollen).
- Two main groups can be recognized within C. intybus subsp. intybus to which all the cultivated types of chicory belong: the first, which refers to the var. foliosum , traditionally includes all the cultivar groups whose commercial products are the leaves (i.e. leaf chicory), while the second regards the var. sativum and comprises all the types whose commercial product, either destined to industrial transformation or direct human consumption, is the root (i.e. root chicory) (for the taxonomic classification of Cichorium intybus botanical varieties, see Lucchin M., Varotto S., Barcaccia G. and Parrini P. (2008). Chicory and Endive.
- transgenic male sterile lines of leaf chicory were produced by expressing the ribonuclease gene RNase from Bacillus amyloliquefaciens (known as BARNASE) under the control of a tapetum-specific promoter originally isolated from tobacco (TA-29) (see Mariani C., De Beuckeleer M., Trueltner J., Leemans J and Goldberg R. B. (1990). Induction of male sterility in plants by a chimaeric ribonuclease gene. Nature, 347: 737-741).
- RNase Bacillus amyloliquefaciens
- Restorer lines for these male-sterile lines were obtained by expressing the gene coding for the so-called BARSTAR, the intracellular inhibitor of BARNASE under control of the same promoter (Denis M., Delourne R., Gourret J. P., Mariani C. and Renerd M. (1993). Expression of engineered nuclear male sterility in Brassica napus : genetics, morphology and sensitivity to temperature. Plant Phys., 101(4): 1295-1304; Reynaerts A., Van de Wiele H., de Sutter G. and Janssens J. (1993). Engineered genes for fertility control and their application in hybrid seed production. Sci. Hort., 55: 125-139).
- Somatic hybridization by means of protoplast symmetric fusion between chicory and the CMS line of sunflower PET-1 was also attempted in order to promote the regeneration of interspecific hybrid plants.
- This kind of CMS in sunflower was identified in an interspecific cross between Helianthus petiolaris and Helianthus annuus , and it was associated with the expression of the mitochondrial gene ORF522, encoding a 15-kD polypeptide.
- the ORF522 gene was originated by a recombination event at the 3′ of atp1 gene and its protein is detectable in flowers of CMS but not of restored lines (Horn R., Köhler R. H. and Zetsche K. (1991).
- a mitochondrial 16-kDA protein is associated with cytoplasmic male sterility in sunflower. Plant Mol.
- Cichorium spp. mainly to characterize commercial varieties and experimental materials, to evaluate the genetic homogeneity and purity, respectively, of inbreds and hybrids, and to investigate phylogenetic relationships between cultivars and cultivar groups of C. intybus and other species, both cultivated and wild, belonging to the same genus.
- Amplified fragment length polymorphism (AFLP) and random amplified polymorphic DNA (RAPD) markers were also used to construct the first genetic map of C. intybus . More recently, a new genetic map was constructed for chicory using simple sequence repeat (SSR or microsatellite) markers by Cadalen et al.
- Cichorium spp. have been exploited for selecting the mother plants of synthetics as well as for determining the distinctiveness, uniformity and stability, i.e. DUS testing, of newly bred varieties.
- molecular markers should also find utility for assessing the genetic homogeneity and homozygosity of inbred lines produced by repeated selfing, measuring the genetic diversity among inbred lines in order to plan crosses and maximize heterosis in the experimental F1 hybrids, and evaluating the genetic purity and heterozygosity of seed stocks of commercial F1 hybrids.
- the present invention discloses male sterile mutants of leaf chicory ( Cichorium intybus subsp. intybus var. foliosum ), induced and developed by the inventors, wherein the new ms trait is inherited as a single recessive nuclear gene (herein denominated generally ms or Cims-1 as opposite to the Ms wild type dominant gene) character.
- the invention discloses also a new polymorphic genetic microsatellite marker tightly linked to the locus where the Ms gene is located. This marker allows to track the mutant allele ms conferring the male-sterility trait of the invention in subsequent selfing and crossing procedures, and to make sure that this trait is advantageously inherited in highly inbred plants in the breeding program suitable for the selection of seed parent lines.
- the identification of a molecular polymorphic marker tightly linked to the locus where the Ms gene is located allows the identification of a ms-linked genotype of the marker and the tracking of the ms gene (also in heterozygous loci) upon generation of a msms seed parent that can conveniently be homozygous also for several other genes of interest.
- the marker is suitable for use in methods for the generation of msms seed parent plants and in methods for the generation of Msms F1 commercial hybrids, wherein the detection of the marker alleles linked to the ms mutation allows following the trait during all the steps of the process.
- mutants of the invention have been developed by the inventors and have been described for the first time at either the cytological and genetic levels, since the analysis of the mutation induced by the inventors has demonstrated that the mutation itself affect a single nuclear gene providing a recessive trait causing male sterility when homozygous (msms). Moreover, the inventors have documented that the mutation leads the microspores of each tetrad to arrest their development at the uninucleate stage, degenerating before their release from the tetrads. At full flowering, in genotypes msms all the microspores of dehiscent anthers were found shapeless, shrunken and much smaller than wild-type ones. The inventors have demonstrated that pollen grains are never produced in mature anthers, demonstrating a full expressivity of the trait with mutants being 100% male sterile.
- the invention hence provides for the first time male sterile mutants of leaf chicory, a molecular marker tightly linked to the ms gene, methods for the identification of mutants in this species carrying the ms mutation at the homozygous or heterozygous state, methods for the production of homozygous msms or heterozygous Msms plants of leaf chicory, parts thereof or derivatives thereof, methods for the production of msms seed parent plants, and methods for the production of heterozygous Msms F1 hybrids of leaf chicory.
- the invention also provides a diagnostic assay for the early screening in leaf chicory populations of the ms mutation herein provided by using the identified polymorphic marker and plant genotypes carrying the ms mutation of the invention.
- FIG. 1 Phenotype of wild-type plants (A-D) and male-sterile mutants (E-H) of red chicory ( Cichorium intybus L.). Details of macroscopic (A, B) and microscopic (C, D) features are given for the wild-type anthers in parallel with mutant anthers (E, F and G, H, respectively).
- FIG. 2 Genetic analysis of male-sterile mutants based on segregation patterns observed in F2 and BC1 progenies. Each of the male sterile mutants was crossed as seed parent with a wild type pollinator belonging to the same subsp. Several F1 plants from each hybrid population were then selfed and crossed in pair-wise combinations in order to obtain segregating F2 progenies. Moreover, F1 plants were also backcrossed as pollen donors with either male sterile mutants belonging to F2 progenies or wild type plants of 51 progenies stemmed from selfing in order to obtain segregating BC1 progenies. These experimental populations were used to establish the inheritance pattern of the mutation and to map the male sterility gene.
- FIG. 3 Flower developmental stages in red chicory (panel A) and patterns of male gametogenesis in the male-sterile mutants in parallel with wild-type plants (panel B).
- the microspores of each tetrad arrest their development at the uninucleate stage, degenerating before their release from the tetrads.
- most of the microspores of dehiscent anthers were found shapeless, shrunken and much smaller than wild-type ones.
- FIG. 4 Microspore size in the male-sterile mutants compared to wild-type plants, expressed as mean value (histograms) with standard error (bars). At the stage of tetrad, the microspores were comparable for their size and shape between mutants and wild-types, whereas mutant microspores at the uninucleate stage proved to be about three times smaller than wild-type ones.
- FIG. 5 Parallel between male gametogenesis in wild-type plants and male-sterile mutants belonging to segregating progenies at flower stages 1-4. Gametogenesis followed a regular pathway in male-fertile plants, giving rise to mature pollen grains, whereas microspores collapsed within each tetrad in the male-sterile plants, without any further developing process. This finding demonstrated that the gene responsible for male-sterility is inherited in the offspring from each mutant by recovering an unaltered maternal genotype, which is always associated to an unchanged phenotype for male-sterility.
- FIG. 6 Results of cytogenetic analyses of male-sterile mutants: different types of meiotic abnormalities were found in the male-sterile mutants compared to wild-types, especially at prophase I, along with chromatin bridges observed in ana-telophase II. Some examples of normal chromosome pairing in wild-types (panel A) and miss-pairing of certain chromosome pairs in male-sterile mutants (panels B-D).
- FIG. 7 Molecular SSR marker diagnostic assay for discriminating male sterile from male fertile plant genotypes.
- This SSR assay is useful as a tool of marker-assisted selection for an early screening of the male sterile plants within segregating progenies, with a genotyping error around 2.9%.
- FIG. 8 Schematic representation of part of the linkage group 4 (i.e. LG4) of Cichorium intybus consensus map containing DNA markers coded as E02M09/163 and EU03H01/178 associated with the ms locus where the mutant gene responsible for male sterility is located in Radicchio (leaf chicory). Each of these two DNA markers includes a microsatellite repeat in their nucleotide sequences as shown in SEQ ID NO1 and SEQ ID NO 5.
- SEQ ID NO 2 CTTGGAGGTGTGAGTGATTCTCGGAGAGTT(TC)CAGAGATCATTGCTT GTGTAATTCTCGCTGATTTCAGTTCATTGTCGTCTCTCTTTGCTGTTTC GTA DNA marker sequence linked to ms mutation in Cichorium spp. containing a variable number of thymine-cytosine repeats (TC)n, with n ranging from 27 to 33 (SEQ ID NO:7) in the ms mutants, that start from nucleotide position 31 (the total length ranges from 141 to 163 nucleotides according to the leaf chicory genotype) (full-length sequence disclosed as SEQ ID NO:6).
- TC thymine-cytosine repeats
- forward primer for marker comprising or consisting of SEQ ID 2 amplification CTTGGAGGTGTGAGTGATTCT 21 (SEQ ID NO: 3) reverse primer for marker comprising or consisting of SEQ ID 2 amplification TACGAAACAGCAAAGAGAGAC 21 (SEQ ID NO: 4) SEQ ID NO 5 GCCATTCCTTTCAAGAGCAGATCTTAAAAGTCTAAAGGGTTTGTGAAT T GTGTGTG CG TGTGTGTGTG TAAATTATTATGGTCCTAAAATGGAT GATATTTGTATTTAAGATCTCCATGCTTGTTTATCAACTCTCTTCTATG ATATGAACAAATATTGTTGCGGTTTTGGGTT DNA marker genetically linked to the ms locus in the linkage group 4 of Cichorium intybus including a variable number of thymine-guanine repeats (TG) with total length in the ms mutants equal to 178 nucleotides.
- TG thymine-guanine repeats
- the present invention describes for the first time a male sterile leaf chicory ( Cichorium intybus subsp. intybus var. foliosum ) mutant, parts or elaborates thereof, wherein the male sterility trait is due to a nuclear recessive mutation (ms) linked to a polymorphic genetic marker comprising SEQ ID NO 1 or SEQ ID NO 2 or consisting of SEQ ID NO 2.
- ms nuclear recessive mutation
- the mutant plants of the invention are plants of “Radicchio” belonging to the species C. intybus subsp. intybus var. foliosum to which refer all the cultivated types of leaf chicory.
- “Radicchio” is the Italian common name that has been adopted by all the most internationally used languages to indicate a very differentiated group of chicories, with red or variegated leaves.
- plant parts it is herein intended parts of the plant carrying nuclear genetic information, starting from the nucleus, cells, tissues, leaves, roots, stems, flowers, and the like whereas by elaborates it is herein intended processed parts of the plant as defined above (e.g. flour, powder, fragments, extracts etc.) wherein said nuclear genetic information is still detectable.
- processed parts of the plant e.g. flour, powder, fragments, extracts etc.
- the invention also provides mutant leaf chicory plants or parts or elaborates thereof, wherein the mutation described above is in heterozygosity (genotype Msms such as F1 hybrids), hence directly detectable only with the marker of the invention.
- mutation Msms such as F1 hybrids
- For indirect detection a number of controlled pollination by means of selfing or back-crossing should be carried out until the homozygous recessive (genotype msms such as in seed parent inbred lines) mutant phenotype is expressed in the segregating F2 or BC1 progeny.
- progeny plants of the msms mutants when segregating progeny plants of the msms mutants are produced, said plants will be either homozygous or heterozygous at the locus for male fertility/sterility, depending on the type of cross-pollination performed to produce the progeny (cfr. FIG. 2 ), and will be detectable at early developmental stages by using the marker herein provided and by comparing the marker alleles of the progeny to the marker alleles of the msms mutant.
- the progeny carrying the mutation in heterozygous form will have one allele (ms) identical to that of the male sterile mutant for the marker of the invention, which will be inherited in the segregating generations.
- the progeny heterozygous for the ms mutation is a F1 commercial hybrid.
- the invention in fact provides F1 hybrids that can be selected for several characters of interest, one of them being the heterozygosity for the ms mutation herein described.
- the mutants of the invention have been characterized in great details for the developmental pathway of micro-sporogenesis and gametogenesis, and the inheritance pattern of the gene underlying the male-sterility trait. Moreover, the fine mapping of the mutant locus has also been accomplished by using molecular markers. Experimental results on the male sterile mutants are presented below in order to describe their phenotype “anthers with no pollen grains” and to discriminate their genotype on the basis of a based on the “polymorphic microsatellite sequence” described below. The potentials of the use of male sterile mutants for breeding new F1 hybrid populations are critically discussed, analyzing also the advantages in comparison to synthetic varieties traditionally constituted in leaf chicory, especially “Radicchio”.
- a male sterile mutant of a plant, parts or derivatives thereof wherein the male sterility trait is controlled by a nuclear recessive mutation (ms).
- the nuclear recessive mutation (ms) may be ascribable to a single gene linked 5.8 cM apart to a polymorphic molecular marker locus finely mapped on linkage group 4 comprising a microsatellite or simple sequence repeat (TC)n in SEQ. ID NO 1 or 2 and the progeny thereof.
- Progeny plants may show either a mutant or a wild-type cytological phenotype for said trait and may be at least heterozygous for said mutation at the ms locus.
- F1 hybrid plants or parts or elaborates thereof obtained using the plant(s), parts or derivatives thereof described herein are provided.
- segregant progeny plants or parts or elaborates thereof obtained using the F1 hybrid plants or parts or elaborates thereof described herein are provided.
- the ms mutations of the invention are recessive mutations of a putatively identified candidate but not yet characterised nuclear gene that the inventors have found to be tightly linked to a new polymorphic molecular marker coded comprising SEQ ID NO 1.
- the marker comprises or consists of SEQ ID NO 2.
- the marker of the invention comprises a Simple Sequence Repeat (SSR) i.e. a (TC)n repeat wherein n is an integer higher than 1 and the polymorphic alleles thereof differ in the number n of repeats of the TC dinucleotide within SEQ ID NO 1 or within SEQ ID NO 2.
- SSR Simple Sequence Repeat
- n is comprised between 27 and 33, i.e. n can be 27, 28, 29, 30, 31, 32, 33 however, the number of repeats can vary from the ones indicated herein without changing the tight linkage of the marker to the locus where the ms trait maps hence alleles where n is different from the ones indicated above are encompassed by the present invention.
- the marker is tightly genetically linked to the locus wherein the ms mutation maps and it is also associated to the linkage group 4 of the Cichorium intybus consensus map along with another Simple Sequence Repeat (SSR) i.e. a (TG)n repeat within SEQ ID NO 5.
- SSR Simple Sequence Repeat
- Linkage is defined as the association between two or more genes such that the traits they control tend to be inherited together (i.e., the genes are transmitted together to the offspring unless they recombine through crossing-over events). More precisely, genes or sequences are genetically associated because they physically reside on the same chromosome. In this specific case, linkage is the association in inheritance of a Mendelian factor (i.e., the gene controlling male sterility/fertility) and a microsatellite marker (i.e., the DNA sequence corresponding to simple nucleotide repeats) so that the segregation pattern of the alleles at these two genomic loci is expected to deviate from independent assortment.
- Mendelian factor i.e., the gene controlling male sterility/fertility
- a microsatellite marker i.e., the DNA sequence corresponding to simple nucleotide repeats
- a linkage group is a group of genes or sequences having their loci on the same chromosome and a linkage map is a map of a given chromosome showing the relative positions of the known genes or sequences on that chromosome of a given species.
- the relative distance between two loci is calculated on the basis of the frequency of recombinant (i.e. non-parental) phenotypes between said loci, which is directly calculated using the frequency of recombinant gametes (i.e. gametes that contain recombinant chromosomes).
- the frequency of recombination is given by the number of recombinants divided the total number of progeny individuals. This frequency is used as a guide in assessing the relative genetic distances between mapped loci on a linkage group.
- the marker comprising SEQ ID NO 1 or SEQ ID NO 2 (or consisting of SEQ ID NO 2), herein denominated also E02M09/99, is linked to the locus where the ms mutation maps, i.e. is at a certain distance from it, on the same chromosome.
- the locus of the ms mutation and the marker of the invention are part of the same linkage group.
- the marker shows a mean recombination frequency with the ms mutation locus (corresponding to the locus of the relative wt gene) of about 5.8%.
- the mutant of the invention can also be defined as a male sterile leaf chicory mutant plants, parts or elaborates thereof, wherein the male sterility trait is due to a nuclear recessive mutation (ms) linked with a mean recombination frequency of about 5.8% to a polymorphic genetic marker comprising SEQ ID NO 1 or comprising or consisting of SEQ ID NO 2.
- ms nuclear recessive mutation
- Msms polymorphic genetic marker
- centimorgan (abbreviated cM), or map unit, is a unit of recombinant frequency for measuring genetic linkage.
- cM centimorgan
- Two markers on a chromosome are 1 cM apart if they have a 1% chance of being separated from each other by a crossing-over in a single generation.
- the centimorgan is often used to infer distance along a chromosome. Assuming that 1 cM is equivalent to about 500 Kb, the distance between the marker comprising SEQ ID NO 1 and the locus for the ms mutation or the wt gene thereof, is of about 3000 Kb.
- the Mendelian factor responsible for male-sterility herein described i.e. the ms mutation and the wt corresponding gene
- the molecular marker E02M09/230 When the datasets for both the trait and the marker were analyzed together, there was a significant deviation in the segregation data from the expected 1:1:1:1 ratio.
- this gene was associated with the AFLP-derived marker E02M09/230 containing a perfect microsatellite motif (TC/GA)n, with n ranging from 27 to 33 (SEQ ID NO:7), that was converted into a SCAR marker with a total length varying up to 163 nucleotides (DNA marker E02M09/163).
- Genetic co-segregation analysis revealed that DNA marker E02M09/163 is located in a chromosome window spanning about 6 cM that belongs to linkage group 4 of the consensus genetic map of chicory (Cadalen T., Mörchen M., Blassiau C., Clabaut A., Scheer I., Hilbert J-L., Hendriks T.
- the two DNA markers and the ms locus are genetically associated in the same linkage group (i.e. LG4), and that this linkage is such that a chromosome window characterized by a total recombination frequency of about 18% can be observed between the two marker loci.
- the two marker loci enclosing the ms gene are at a genetic distance of about 19 cM.
- our E02M09/163 and EU03H01/178 markers are mapped about 6 cM and 13 cM apart from the ms locus, respectively.
- the probability that both markers genetically recombine from the ms locus because of the occurrence of a double crossing-over is therefore very low being less than 1%.
- the ms mutation underlying male-sterility of Radicchio (leaf chicory) plants will be genetically associated with a microsatellite DNA marker, including (TC/GA)n nucleotide repeats in SEQ ID NO 1 and/or in SEQ ID NO 2 with n varying in number from 27 or 33 (SEQ ID NO:7), that is physically positioned in the linkage group 4 of the Cichorium intybus genome consensus map.
- the ms mutation underlying male-sterility of Radicchio (leaf chicory) plants will be genetically associated also with another DNA marker, including a sequence that contains (TG/CA)nCG/CG(TG/CA)n nucleotide repeats reported in SEQ ID NO 5, that is genetically mapped in the linkage group 4 of the Cichorium intybus genome consensus map.
- the invention further provides a method for the selection of mutant plants of leaf chicory that are homozygous or heterozygous for a mutation inducing nuclear recessive male sterility (ms).
- the method which is based on the detection of the molecular marker E02M09/163, includes the following steps:
- the method herein described is based on the tight genetic linkage between the marker E02M09/163, and the locus wherein the ms mutation of the invention maps.
- the two loci map in the same linkage group and are at an estimated distance of about 6 cM.
- the mutants selected with the method described above will be heterozygous (Msms) or homozygous (msms) for the male sterile mutation.
- the possibility of comparison with a msms mutant of reference allows the breeder to follow the presence of the ms trait throughout the segregating generations and to finally obtain, when desired, a new genotype being mutant homozygous for the ms allele having also other selected traits of interest.
- the new male sterile mutant may differ from the msms mutant of reference by the presence of specific alleles for a certain number of genes of interest.
- the method of the invention can be used to follow the ms trait in breeding programs where several crosses are performed in order to obtain individuals carrying a desired genotype for several genes and where the ms mutation is to be maintained.
- genotyping of the mutant of reference and of the plants under assay can be carried out with any technique known to the skilled person for the detection of polymorphisms for simple sequence repeats.
- amplification of a DNA region, also called amplicon, including the repeat is carried out and the number of repeats is assessed by several existing techniques.
- amplicon refers, in the present description, to a nucleotide fragment generated by means of PCR amplification of a DNA sample used as template.
- Suitable primers for amplification can be readily generated starting from SEQ ID NO 1 or 2 by the aid of freely available or commercial programs for primers design or by standard techniques for the design of amplification primers.
- the amplification may be carried out upon DNA extraction from the sample to be analysed, or directly on material collected from the sample diluted or suspended in the PCR mixture. Standard DNA extraction techniques for plants known in the art can be used.
- amplicons length may be verified, by capillary electrophoresis techniques; by analysis by dissociation curve, by sequencing the amplicons, by electrophoresis of the amplicons on agarose gel or on polyacrylamide gel or by any other technique known to the skilled person.
- capillary electrophoresis it is meant an electrophoretic technique envisaging the use of fused silica microcapillary tubing, with an internal diameter comprised between 10 and 100 microns, with a length between 30 and 50 cm. Said tubing is filled with a (gel-like) substance acting as a molecular sieve.
- the matrix may be polyacrylamide, dimethylacrylamide or other linear polymers, such as polyethylene oxide or hydroxyethyl cellulose.
- the amplicons are obtained for the samples of interest, they can be analysed as described above and comparison to the reference msms genotype for the marker of the invention can be carried out. Plants sharing at least one allele of the marker of the invention with the msms genotype of reference will be selected.
- the amplification can be carried out using primers of SEQ ID NO 3 and SEQ ID NO 4, corresponding, respectively, to a stringent forward primer (5′-CTTGGAGGTGTGAGTGATTCT-3′) SEQ ID NO 3 and reverse primer (5′-TACGAAACAGCAAAGAGAGAC-3′) SEQ ID NO 4 amplifying SEQ ID NO 2.
- amplification of the molecular marker of interest is obtained and includes a microsatellite showing a perfect dinucleotide repetition of the motif (TC/GA)n.
- SSR diagnostic microsatellite
- PCR experiments were conducted in a 20 ⁇ l total volume, including 10 mM Tris-HCl, 50 mM KCl, 1.5 mM MgCl2, 200 mM of each dNTP, 3 pmol of primer forward, 8 pmol of primer reverse, 6 pmol M13-labeled primer, 1 U Taq DNA polymerase (GE Healthcare) and 25 ng of genomic DNA as template.
- Amplification reactions were performed in a 9700 Thermal Cycler (Applied Biosystems): the temperature profile consisted of an initial denaturation step of 5 min at 95° C.
- DNA fragment analysis was carried out using a fully automated capillary electrophoresis system (Applied Biosystems 3130) and SSR patterns were visualized and scored in replicated analysis using the software GeneScan® v. 2.1 e Genotyper® v. 2.0 (Applied Biosystems).
- n ranges from 27 to 33 and the amplicons obtained by amplification with the primers of SEQ ID 3 and 4 above are of a size range of about 160-170 bp.
- the invention also provides a method for the production of mutant male sterile seed parental lines of leaf chicory, including all radicchio biotypes, wherein the male sterility is a nuclear recessive male sterility due to the mutation of a nuclear gene (ms) linked to the marker of the invention, comprising the steps of:
- the method above is hence a method for the selection of male sterile mutants of all forms of leaf chicory, including all radicchio biotypes (belonging to Cichorium intybus subsp. intybus var. foliosum ) wherein the male sterility mutation is the nuclear recessive mutation of the invention.
- Said method allows the selection of desired seed parent plants that, as described above, are plants to be used as female, i.e. plants that need pollination by a pollen donor plant, and that will produce the seeds of the plants of commercial interest.
- the method for making the seed parent of the invention can comprise several hybridization and selection steps relating to other characters and that the monitoring of the ms trait can be carried out at each of said steps if desired, by the method for the selection of a mutant carrying the ms mutation indicated above, wherein the genotyping of the msms reference genotype can be carried out only once in order to determine said genotype.
- the method can hence been described as a method for the production of mutant male sterile seed parents of all forms of leaf chicory, including all radicchio biotypes, wherein the male sterility is a nuclear recessive male sterility due mutation of a nuclear gene (ms) linked to the marker of the invention, comprising the steps of:
- the seed parent is advantageously a male sterile plant, hence the method of the invention allows to set up breading programs wherein the male sterility mutation of the invention can be followed throughout several controlled crosses until the desired seed parent is obtained said seed parent being, hence, advantageously male sterile.
- the invention relates to a method for the production of mutant F1 hybrids of all forms of leaf chicory, including all radicchio biotypes (belonging to Cichorium intybus subsp. intybus var. foliosum ) wherein said hybrids are fertile and heterozygous for a mutation in a gene inducing nuclear recessive male sterility (ms) linked to the marker of the invention comprising the steps of:
- the invention also provides a method applicable to a full breeding program, wherein the parental plants that will generate the F1 hybrids having the commercial traits of interest, can be tracked for the ms mutation of the invention throughout the whole selection process aimed to obtaining the assembly of all the commercial traits of interest in the parent plants so to generate, in the end, msms seed parents and MsMs pollen donors.
- the method can comprise several hybridization and selection steps relating to other characters and the monitoring of the ms trait can be carried out at each of said steps if desired, by the method for the selection of a mutant carrying the ms mutation indicated above, wherein the genotyping of the msms reference genotype can be carried out only once in order to determine said genotype.
- the invention also relates to a method for the production of mutant F1 hybrids of all forms of leaf chicory, including all radicchio biotypes (belonging to Cichorium intybus subsp. intybus var. foliosum ) wherein said hybrids are fertile and heterozygous for a mutation in a gene inducing nuclear recessive male sterility (ms) comprising the steps of:
- the methods of the invention have a very low probability of error as their reliability is of about 95%, hence they are highly effective in the ms mutation selection as explained above.
- All the methods herein disclosed can be carried out as described above, hence by amplification of the marker comprising SEQ ID NO 1 or SEQ ID NO 2 (or consisting of SEQ ID NO 2) and determination of the number n of the SSR or simple sequence repeat (TC)n for each allele in the plants or parts thereof assayed and in the msms mutants (wherein the mutation is the mutation of the invention, linked to the marker comprising SEQ ID NO 1 or SEQ ID NO 2) of reference.
- suitable primers are represented by the primers of SEQ ID NO 3 and SEQ ID NO 4 wherein the PCR conditions can be the ones described above.
- male sterile mutants of leaf chicory were recently induced by standard mutational techniques and were isolated on the basis of morphological observations of anthers ( FIG. 1 ).
- the male-sterile mutants analyzed in this study were named L11ms, IG9 ms, CS1ms and CS2 ms. It is worth mentioning that the male sterile mutants were discovered within local varieties of Radicchio stemmed from recurrent phenotypic selection programs. In particular, the three populations from which they originate have been bred through genetic selection based on progeny tests performed using mother plants chosen for uniformity and superiority of their morphological and agronomic traits.
- DAPI a fluorescent stain that binds strongly to A-T rich regions in DNA.
- Anther heads isolated from five flowers for each of the male-sterile mutants and the wild-types were squashed on a microscope slide and treated with 10 ⁇ l of staining solution (DAPI 5 ⁇ g/ml). After an incubation of 10 min, a detailed observation of stained anthers was done by a Leica DM4000B imagine microscope using the appropriate filter combination for DAPI fluorescent detection.
- anther specimens of mutants and wild-types were treated with citrate buffer (10 mM citric acid, 10 mM sodium citrate, pH 4.5) for 3 min and incubated in a six times diluted pectolytic enzyme mixture containing 1% pectolyase Y23, 1% cellulase RS and 1% cytohelicase (Sigma Aldrich, http://www.sigmaaldrich.com) in 10 mM citrate buffer at 37° C. for about 1-2 hours, according to the anther stage.
- citrate buffer 10 mM citric acid, 10 mM sodium citrate, pH 4.5
- Anther preparations were squashed on microscope slides using a drop of purified and deionized water (Milli-Q Integral Water Purification System, http://www.millipore.com) and then transferred on a hot plate at 45° C. Cells were spread on microscope slides using a teasing needle by adding one drop of 45% acetic acid, then maintained at 45° C. for 2 min and washed with Carnoy's solution. Each slide was dried on the hot plate at 45° C. and specimens were stained with DAPI.
- Cytological observations of male meiosis and gametogenesis as well as karyological analysis of meiocyte chromosomes were made under natural and fluorescent light using a photomicroscope (Zeiss Axiophot photomicroscope, www.zeiss.com) equipped with epifluorescence illumination and single-band filters for DAPI. Photograph films were scanned at 1,200 dpi for digital image processing with Adobe Photoshop® CS4 (Adobe Inc., U.S.A.).
- Each of the male sterile mutants was crossed as seed parent with a wild type pollinator belonging to the same population.
- F1 plants from each hybrid population were then selfed and crossed in pair-wise combinations in order to obtain segregating F2 progenies.
- F1 plants were also backcrossed as pollen donors with either male sterile mutants belonging to F2 progenies or wild type plants of S1 progenies stemmed from selfing in order to obtain segregating BC1 progenies ( FIG. 2 ).
- the experimental populations segregating for the male sterility/fertility trait were composed of about 100 plants for each of the four mutants. These populations were used for genetic analyses in order to establish the inheritance pattern of the mutation (e.g., dominant/recessive nuclear vs. cytoplasmic) and to finely map the male sterility gene using microsatellite markers.
- a total of 118 F2 progeny plants and 92 BC1 progeny plants segregating, respectively, 3:1 and 1:1 for the male fertility vs. sterility trait were used for mapping the ms locus using SSR markers.
- 100 plants of the segregating progenies of mutant IG9 ms were also analyzed in order to validate molecular markers tightly co-segregating with male sterility.
- Total genomic DNA was isolated from 100 mg of fresh leaf tissue using the DNeasy® Plant mini-kit (QIAGEN, www.qiagen.com) following the recommendations of the manufacturer.
- the DNA pellets were washed twice with 70% ethanol, dried and resuspended in 100 ⁇ l of TE 0.1 ⁇ buffer (Tris-HCl 100 mM, EDTA 0.1 mM pH 8).
- the purity was calculated by the O.D.260/O.D.280 ratio and by O.D.210-O.D.310 pattern (as described in Barcaccia G., Pallottini L., Soattin M., Lazzarin R., Parrini P. and Lucchin M. (2003). Genomic DNA fingerprints as a tool for identifying cultivated types of radicchio ( Cichorium intybus L.) from Veneto, Italy. Plant Breeding 122, 178-183.).
- a subset of 48 progeny plants with a contrasting microgametogenesis pattern (i.e., 24 male sterile plants and 24 male sterile plants) were selected and used for performing a bulked segregant analysis, BSA in the attempt to identify molecular markers linked to the male-sterility trait.
- Genomic DNA bulks of 12 plants each from two progeny sets were prepared by combining equal amounts of DNA from male fertile and male sterile plants. All bulked DNA samples were investigated by AFLP markers using the parental lines as controls.
- Genomic AFLP fingerprinting was performed using the protocol of Vos et al. (1995) (Vos P., Hogers R., Bleeker M., Reijans M., Van de Lee T., Homes M., Frijters A., Pot J., Peleman J, Kuiper M. and Zabeau M. (1995).
- AFLP A new technique for DNA fingerprinting. Nucleic Acids Research, 23: 4407-4414.) with modifications described by Barcaccia et al. (2003) (Barcaccia G., Pallottini L., Soattin M., Lazzarin R., Parrini P. and Lucchin M. (2003).
- Genomic DNA fingerprints as a tool for identifying cultivated types of radicchio ( Cichorium intybus L.) from Veneto, Italy. Plant Breeding, 122: 178-183.).
- AFLP analysis was based on the detection of EcoRI-MseI genomic restriction fragments by PCR amplification with 9 different primer combinations having three selective nucleotides (E+CAC, E+CCA, E+CTG and M+ATC, M+AGG and M+AAG), chosen during preliminary tests according to their ability to find homologous binding sites in red chicory templates.
- the pre-amplified DNA was diluted 1:1 in Tris-EDTA buffer and was used as template for hot-PCRs with a MseI primer carrying three selective nucleotides in combination with a EcoRI radiolabelled primer, carrying two selective nucleotides at the 3′ end.
- Selective amplification was carried out under cycling conditions which begins with one cycle at 94° C. for 30 s, 65° C. for 30 s, and 72° C. for 60 s.
- the annealing temperature was then reduced each cycle by 0.7° C. according to a touch-down profile of 13 cycles to reach the optimal annealing temperature of 56° C. Twenty-three cycles were run to complete the final amplification at 94° C. for 30 s, 56° C. for 30 s and 72° C. for 60 s.
- PCR reactions were stopped with equal volume of loading buffer (98% formamide, 10 mM EDTA, 0.025% bromophenol blue, 0.025% xylene cyanol) and denatured at 94° C. for 5 min.
- loading buffer 98% formamide, 10 mM EDTA, 0.025% bromophenol blue, 0.025% xylene cyanol
- the labelled, restricted and selectively amplified DNA fragments were separated by electrophoresis on 5% denaturing polyacrylamide gels with 8 M urea at 80 W constant power using a standard DNA sequencing unit Sequi-Gen GT-system (BIO-RAD). Gels were dried at 80° C. for 1 h and then visualized by autoradiogram after overnight exposure on an X-ray film at ⁇ 80° C. using intensifying screens.
- the AFLP fragment analysis was performed using the 1D® Image analysis software (Kodak Digital Science). Overall data were recorded as a binary matrix by assigning the molecular weight to each quantitatively polymorph
- Microsatellite (SSR) loci analysis was carried out following an already tested PCR protocol (Ambrosi D. G., Galla G., Purelli M., Barbi T., Fabbri A., Goaletti S., Sharbel T. F. and Barcaccia G. (2010). DNA markers and FCSS analyses shed light on the genetic diversity and reproductive strategy of Jatropha curcas L. Diversity, 2: 810-836.) with some changes to adapt it to red chicory templates. The detection was performed with the use of the 5′ M13-tailed primer method (Hayden et al., 2008) (see Hayden M. J., Nguyen T. M., Whatman A., McMichael G. L., Chalmers K. J. (2008).
- DNA fragments were visualized by capillary electrophoresis after amplification reactions performed with the universal M13 primer (the sequence of the tail is the following: 5′-TTGTAAAACGACGGCCAGT-3′ (SEQ ID NO:9)) labeled with a HEX, FAM or TAMRA fluorophore (by Life Technologies).
- PCR experiments were conducted in a 20 ⁇ l total volume, including 10 mM Tris-HCl, 50 mM KCl, 1.5 mM MgCl2, 200 mM of each dNTP, 3 pmol of primer forward, 8 pmol of primer reverse, 6 pmol M13-labeled primer, 1 U Taq DNA polymerase (GE Healthcare) and 25 ng of genomic DNA as template. All individual DNA samples were then investigated with 9 SSR markers belonging to as many mapped loci, one for each of the nine linkage groups (i.e., basic chromosomes) of the genetic map recently constructed by Cadalen et al.
- 9 SSR markers belonging to as many mapped loci, one for each of the nine linkage groups (i.e., basic chromosomes) of the genetic map recently constructed by Cadalen et al.
- JOINMAPTM version 2.0 Software for the calculation of genetic linkage maps. CPRO-DLO, Wageningen, The Netherlands.) using the cross pollination (CP) population type option (i.e., segregating populations resulting from a cross between two heterogeneous parents that were heterozygous and/or homozygous at the loci being tested). The association between microsatellite markers and male sterility was assessed by recording the target ms locus as a putative monogenic marker fully co-segregating with the trait being mapped.
- CP cross pollination
- SSR diagnostic microsatellite
- PCR experiments were conducted in a 20 ⁇ l total volume, including 10 mM Tris-HCl, 50 mM KCl, 1.5 mM MgCl2, 200 mM of each dNTP, 3 pmol of primer forward, 8 pmol of primer reverse, 6 pmol M13-labeled primer, 1 U Taq DNA polymerase (GE Healthcare) and 25 ng of genomic DNA as template Amplification reactions were performed in a 9700 Thermal Cycler (Applied Biosystems): the temperature profile consisted of an initial denaturation step of 5 min at 95° C. followed by 40 cycles of 30 sec at 95° C., 30 sec at annealing temperature of 55-58° C., and 30 second at 72° C., followed in turn by 7 min at 72° C.
- DNA fragment analysis was carried out using a fully automated capillary electrophoresis system (Applied Biosystems 3130) and SSR patterns were visualized and scored in replicated analysis using the software GeneScan® v. 2.1 e Genotyper® v. 2.0 (Applied Biosystems).
- the AFLP-derived amplicons corresponding to the marker E02M09/230 identified and characterized in the chicory progenies were recovered from the agarose gels, subcloned into plasmid vectors and sequenced in order to obtain information on the whole genomic sequence. PCR reactions were performed for both strands using three genomic DNA templates belonging to male sterile and male fertile plants of each segregating population.
- the sequence of the SCAR marker developed from the AFLP amplicon genetically linked with the male sterility trait, that correspond to the DNA marker E02M09/163, is the following:
- the molecular marker of interest proved to include a microsatellite showing a perfect dinucleotide repetition of the motif (TC/GA)n, with n ranging from 27 to 33 (SEQ ID NO:7).
- FIG. 7 shows SSR genotypes detected in the progeny plants of segregating populations: male-sterile plants were homozygous AA or BB, with marker alleles of 160 and 162 bp, respectively, whereas male fertile-plants could be either heterozygous AD or BC and homozygous DD or CC, with marker alleles of 170 and 168 bp, respectively.
- SSR assay developed in this study can be profitably adopted as a tool of marker-assisted breeding and exploited for an early screening of the T&T® male-sterile plants within segregating progenies stemmed from back-crosses with a genotyping error around 2.9%.
- the 20-mer forward and reverse primers used for assaying the SSR locus coded as EU03H01, containing an imperfect microsatellite motif (TG)nCG (TG)n, and found associated to the linkage group 4 of the Cichorium intybus consensus map are the following: 5′-GCCATTCCTTTCAAGAGCAG-3′ (SEQ ID NO:10) and 5′-AACCCAAAACCGCAACAATA-3′ (SEQ ID NO:11) (Cadalen T., Mörchen M., Blassiau C., Clabaut A., Scheer I., Hilbert J-L., Hendriks T. and Quillet M-C. (2010). Development of SSR markers and construction of a consensus genetic map for chicory ( Cichorium intybus L.). Molecular Breeding, 25: 699-722).
- cytoplasmic related to a mitochondrial gene
- nuclear which can be associated to either a dominant or a recessive gene.
- F1 progenies had to be composed exclusively of male sterile plants (with cytoplasm of S type), whereas in case of nuclear origin, two were the expected results: all F1 progeny plants (with a heterozygous genotype Msms) had to manifest male-sterility, for a trait controlled by a dominant Mendelian factor (i.e., Ms), or male-fertility, for a trait controlled by a recessive Mendelian factor (i.e., ms).
- Ms a dominant Mendelian factor
- ms recessive Mendelian factor
- microsporogenesis proceeds normally up to the development of microspore tetrads. Then the microspores arrested their development at the uninucleate stage, as documented in FIG. 3 using a parallel with unrelated wild-type plants.
- cytological observations revealed that microspores degenerate before their release from the tetrads showing a collapse of the exine.
- most of the microspores were found arranged in tetrads while some others were released, becoming shapeless even though the cytoplasm stained well with aceto-carmine.
- the chromosome behaviour of male-sterile mutants was also investigated during meiosis: the male meiocyte chromosomes were further analyzed by means of DAPI staining in both wild-type and mutant flowers. Different forms of meiotic abnormalities were found in the male-sterile mutants compared to wild-types, especially at prophase I. In fact, during pachytene, the stage when chiasmata take place and crossing-over occurs between non-sister chromatids of homologous chromosomes, abnormal pairings and chromosomal loops were observed in several sites. Moreover, chromatin bridges were also observed in ana-telophase II. FIG.
- FIG. 6 shows some examples of normal chromosome pairing in wild-types (panel A) and miss-pairing of certain chromosome pairs in male-sterile mutants (panels B-D).
- the main aberrant feature was recovered at pachytene stage when the homologue chromosomes reached their full pairing. It was evident that in the mutant, the homologues were not completely pairing each other and aberrant structures characterized by one or more loops, due to partial or aspecific pairing between homologous chromosomes, were often observed (see white arrows in panels B-D of FIG. 6 ).
- chromatin bridges i.e. bridges made of chromatin occurring between newly forming cells, were found in the male-sterile mutants ( FIG. 6 , panels E-L).
- the Mendelian factor responsible for male-sterility was found tightly linked with the molecular marker coded as E02M09/230.
- E02M09/230 The molecular marker coded as E02M09/230.
- recombination events were apparently possible in the chromosome block carrying the male-sterility gene.
- this gene was associated with the marker E02M09/230 in a chromosome window likely characterized by active crossing-over sites and densely saturated by expressed sequence tags.
- the mean recombination frequency between the male-sterility trait and the microsatellite marker was equal to 5.8%, corresponding to about 6 cM after correction with the Kosambi's function. This means that the size of the chromosome window covering the ms locus may be around 3,000 Kb (assuming 500 Kb/cM).
- this DNA marker belongs to the distal part of linkage group 4 being mapped on a chromosome window of about 6 cM apart from the male-sterility (ms) locus.
- the marker locus coded as EU03H01/178 containing an imperfect microsatellite motif (TG)nCG(TG)n, with total n varying up to 11 (SEQ ID NO:8), was found associated to the male-sterility (ms) trait, showing a genetic distance around 13 cM.
- the two DNA markers i.e. E02M09/163 and EU03H01/178
- the ms gene are genetically associated in the same linkage group (i.e. LG4), and that this linkage is such that a chromosome window characterized by a total recombination frequency of 18% can be observed between the two marker loci.
- the two marker loci enclosing the ms gene are at a genetic distance of about 19 cM ( FIG. 8 ).
- the probability that both markers genetically recombine from the ms locus because of the occurrence of double crossing-overs is lower 1%.
- the new male-sterility trait obtained and demonstrated by the inventors in chicory mutants is controlled by a single nuclear gene (ms) that acts at the recessive status.
- ms nuclear gene
- all crosses between male-sterile mutants and wild-type pollinators resulted in 100% male-fertile F1 progenies (Msms)
- F2 and BC1 progenies segregated for this trait being composed of both male-fertile and male-sterile plants, with ratios equal to 3 (25% MsMs and 50% Msms):1 (25% msms) and 1 (50% Msms):1 (50% msms), respectively.
- mutants characterized by the lack of chromosome pairing during the first meiotic prophase i.e., asynapsis
- mutants in which chromosomes initially pair in early meiotic prophase but fail to remain paired at later meiotic stages i.e., desynapsis
- mutant phenotype is attributable to a gene expressed in an anther-specific manner
- a new PCR-based assay that can be profitably adopted for an early screening of the male-sterile plants within segregating progenies has been implemented by the inventors, with a genotyping error lower than 1%.
- the gene responsible for male-sterility was found genetically linked to a new molecular marker (herein denominated E02M09/230), about 6 cM apart from the ms locus.
- the molecular marker linked to male-sterility was sequenced and its analysis disclosed a perfect dinucleotide microsatellite of the repetitive motif (TC/GA)n, with n being variable and ranging, in most observed cases, from 27 to 33 (SEQ ID NO:7).
- an SSR assay for the detection of this marker whose size ranges around 160-170 bp, was implemented by the design of a specific pair of primers of SEQ ID NO 3 and 4.
- the male-sterile plants were homozygous for the smaller marker alleles, whereas male fertile-plants could be either heterozygous or homozygous for marker alleles of larger size.
- the PCR-based assay herein described will find application not only for the marker-assisted selection of male-sterile seed parents but also for the genetic identification and legal protection of these valuable mutant genotypes of red chicory. Since the history of plant breeding after the rediscovery of Mendel's laws, the exploitation of heterosis is an effective approach to increase crop yields.
- F1 hybrid populations and varieties in major crops such as cereals and vegetables can show more than a 100% yield advantage over the best conventional ones under the same cultivation conditions. Difficulties in breeding elite male sterile lines and producing commercial hybrid seeds hamper the development of F1 hybrid populations. An important role in chicory breeding could be played by male-sterility in hybrid seed production: this is particularly true in “radicchio” since self-incompatibility of parental lines was found inadequate for reliable production of F1 hybrids.
- non-engineered male-sterility in this species i.e., non OGM
- non OGM non-engineered male-sterility in this species
- the discovery and analysis of non-engineered male-sterility in this species will open new frontiers for breeding new F1 populations of radicchio, in particular, and of chicory, in general, provided that such trait can be successfully transferred to elite inbred lines and precociously identified by molecular diagnostic assays suitable to perform marker-assisted selection as from the teachings of the present disclosure.
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Abstract
Description
| |
TGAGTGATTCTCGGAGAGTT(TC)CAGAGATCATTGCTTGTGTA |
DNA marker sequence linked to ms mutation in Cichorium spp. containing a variable number of thymine-cytosine repeats variable (TC)n
|
CTTGGAGGTGTGAGTGATTCTCGGAGAGTT(TC)CAGAGATCATTGCTT |
GTGTAATTCTCGCTGATTTCAGTTCATTGTCGTCTCTCTTTGCTGTTTC |
GTA |
DNA marker sequence linked to ms mutation in Cichorium spp. containing a variable number of thymine-cytosine repeats (TC)n, with n ranging from 27 to 33 (SEQ ID NO:7) in the ms mutants, that start from nucleotide position 31 (the total length ranges from 141 to 163 nucleotides according to the leaf chicory genotype) (full-length sequence disclosed as SEQ ID NO:6).
forward primer for marker comprising or |
consisting of |
CTTGGAGGTGTGAGTGATTCT 21 (SEQ ID NO: 3) |
reverse primer for marker comprising or |
consisting of |
TACGAAACAGCAAAGAGAGAC 21 (SEQ ID NO: 4) |
|
GCCATTCCTTTCAAGAGCAGATCTTAAAAGTCTAAAGGGTTTGTGAATT |
GTGTGTGTGCGTGTGTGTGTGTGTAAATTATTATGGTCCTAAAATGGAT |
GATATTTGTATTTAAGATCTCCATGCTTGTTTATCAACTCTCTTCTATG |
ATATGAACAAATATTGTTGCGGTTTTGGGTT |
DNA marker genetically linked to the ms locus in the
-
- genotyping the chicory plants, leaves or parts thereof by analysing their DNA for the simple sequence repeat (TC)n in
SEQ ID NO 1 orSEQ ID NO 2; - comparing the genotypes thus obtained to a male sterile genotype of reference (msms) for said simple sequence repeat (TC)n target DNA regions; and
- selecting the plants having at least one marker allele of said DNA repeat where n is equal to the n of said male sterile genotype of reference.
- genotyping the chicory plants, leaves or parts thereof by analysing their DNA for the simple sequence repeat (TC)n in
-
- genotyping the chicory plants, leaves or parts thereof by analysing their DNA for the simple sequence repeat (TC)n in
SEQ ID NO 1 orSEQ ID NO 2; - comparing the genotypes thus obtained to a male sterile genotype of reference (msms) for said simple sequence repeat (TC)n target DNA regions; and
- selecting the plants having both marker alleles of said DNA repeat where n is equal to the n of said male sterile genotype of reference.
- genotyping the chicory plants, leaves or parts thereof by analysing their DNA for the simple sequence repeat (TC)n in
-
- genotyping the chicory plants, leaves or parts thereof by analysing their DNA for the simple sequence repeat (TC)n in
SEQ ID NO 1 orSEQ ID NO 2; - comparing the genotypes so obtained to a male sterile genotype of reference (msms) for said simple sequence repeat (TC)n target DNA regions;
- selecting plants having at least one allele for said DNA repeat wherein n is equal to the n of said male sterile genotype of reference,
- submitting said plants to hybridization and selection for other traits, repeating said genotyping on said plants and comparing the genotype thus obtained to said genotype of reference, and
- selecting the plants having both alleles of said sequence repeat where n is equal to the n of said male sterile genotype of reference.
- genotyping the chicory plants, leaves or parts thereof by analysing their DNA for the simple sequence repeat (TC)n in
-
- selecting plants having at least one allele for said sequence repeat wherein n is equal to the n of said male sterile genotype of reference,
- submitting said plants to hybridization and selection for other traits, repeating said genotyping on said plants and comparing the genotype thus obtained to said genotype of reference, can be repeated several times until the desired genotype for the other traits is obtained.
-
- genotyping the chicory plants, leaves or parts thereof by analysing their DNA for the simple sequence repeat (TC)n in
SEQ ID NO 1 orSEQ ID NO 2, - comparing the genotypes so obtained to a male sterile genotype of reference for said simple sequence repeat (TC)n target DNA regions,
- selecting the plants having both marker alleles of said sequence repeat where n is equal to the n of said male sterile genotype of reference thus obtaining male sterile (msms) seed parent plants,
- selecting the plants having both marker alleles of said sequence repeat where n is different from the n of said male sterile genotype of reference thus obtaining male fertile (MsMs) pollen donor plants, and
- crossing said seed parent plants with said pollen donor plants and collecting the F1 seed thus obtained.
- genotyping the chicory plants, leaves or parts thereof by analysing their DNA for the simple sequence repeat (TC)n in
-
- genotyping the chicory plants, leaves or parts thereof by analysing their DNA for the simple sequence repeat (TC)n in
SEQ ID NO 1 orSEQ ID NO 2; - comparing the genotypes thus obtained to a male-sterile genotype of reference (msms) for said simple sequence repeat (TC)n target DNA regions,
- selecting plants having at least one allele for said sequence repeat wherein n is equal to the n of said male sterile genotype of reference,
- submitting said plants to hybridization and selection for other traits, repeating said genotyping on said plants and comparing the genotype thus obtained to said genotype of reference,
- selecting the plants having both marker alleles of said sequence repeat where n is equal to the n of said male sterile genotype of reference thus obtaining male sterile (msms) seed parent plants,
- selecting the plants having both marker alleles of said sequence repeat where n is different from the n of said male sterile genotype of reference thus obtaining male fertile (MsMs) pollen donor plants, and
- crossing said seed parent plants with said pollen donor plants and collecting the F1 seed thus obtained.
- genotyping the chicory plants, leaves or parts thereof by analysing their DNA for the simple sequence repeat (TC)n in
-
- selecting plants having at least one marker allele for said sequence repeat wherein n is equal to the n of said male sterile genotype of reference,
- submitting said plants to crossing and selection for other traits, repeating said genotyping on said plants and comparing the genotype thus obtained to said genotype of reference, can be repeated several times until the desired genotype for the other traits is obtained.
CTTGGAGGTGTGAGTGATTCTCGGAGAGTT(TC)nCAGAGATCATTGCT |
TTGGTAATTCTCGCTGATTTCAGTTCATTGTCGTCTCTCTTTGCTGTTT |
CGTA (SEQ ID NO: 6). |
The molecular marker of interest proved to include a microsatellite showing a perfect dinucleotide repetition of the motif (TC/GA)n, with n ranging from 27 to 33 (SEQ ID NO:7). As a consequence, a novel SSR assay for the detection of this marker, which includes the basic dinucleotide repeat TC/GA and whose size ranges from 141-171 bp in relation to the genotypes, was implemented by the design of a specific and stringent forward primer (5′-CTTGGAGGTGTGAGTGATTCT-3′(SEQ ID NO:3)) and reverse primer (5′-TACGAAACAGCAAAGAGAGAC-3′ (SEQ ID NO:4)).
TABLE 1 |
Segregation ratios observed in the F2 and BC1 populations bred for |
each of the male-sterile mutants along with chi-square values. |
Expected ratios | Observed ratios |
male- | male- | male- | male- | Chi- | |||
Progeny | Progeny | fertile | sterile | fertile | sterile | square | |
Mutants | type | size | plants | plants | plants | plants | values |
CS1ms | F2 | 107 | 80 | 27 | 82 | 25 | 0.153 | |
CS2ms | F2 | 92 | 69 | 23 | 71 | 21 | 0.232 | |
| F2 | 100 | 75 | 25 | 78 | 22 | 0.480 | |
L11ms | F2 | 84 | 63 | 21 | 66 | 18 | 0.571 | |
Overall | F2 | 383 | 287 | 96 | 297 | 86 | 1.324 | |
CS1ms | BC1 | 94 | 47 | 47 | 49 | 45 | 0.170 | |
CS2ms | BC1 | 102 | 51 | 51 | 54 | 48 | 0.353 | |
| BC1 | 88 | 44 | 44 | 41 | 47 | 0.409 | |
L11ms | BC1 | 96 | 48 | 48 | 43 | 53 | 1.042 | |
Overall | BC1 | 380 | 190 | 190 | 187 | 193 | 0.095 | |
In the Mutants Male Gametogenesis is Arrested at the Stage of Uninucleate Microspores
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FR2832290A1 (en) | 2001-11-16 | 2003-05-23 | Nunhems Zaden Bv | Cultivated Cichorium plant, useful for production of hybrid seeds and plants, has a male sterility allele at locus MS, linked to specific markers |
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WO1997045548A1 (en) | 1996-05-31 | 1997-12-04 | Florimond Desprez Veuve Et Fils | Recombinant plant genome, comprising specific chicory genes and a nucleotide sequence conferring male sterility, and its use. |
FR2832290A1 (en) | 2001-11-16 | 2003-05-23 | Nunhems Zaden Bv | Cultivated Cichorium plant, useful for production of hybrid seeds and plants, has a male sterility allele at locus MS, linked to specific markers |
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US20140157448A1 (en) | 2014-06-05 |
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